QC Report


general
Report generated at2022-10-07 07:01:53
TitleCTCF_DLPFC-NEG
DescriptionChIP-seq for CTCF_DLPFC-NEG
Pipeline versionv1.3.6
Pipeline typetf
Genomehg38
Alignerbowtie2
Sequencing endedness{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}, 'ctl2': {'paired_end': False}}
Peak callerspp

Alignment quality metrics


SAMstat (raw unfiltered BAM)

rep1rep2ctl1ctl2
Total Reads28709786284197064000000040000000
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads15648829251398293450157339343175
Mapped Reads (QC-failed)0000
% Mapped Reads54.5000000000000188.586.398.4
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Marking duplicates (filtered BAM)

rep1rep2ctl1ctl2
Unpaired Reads14007094225952712990696833900725
Paired Reads0000
Unmapped Reads0000
Unpaired Duplicate Reads55861093360228767973916411
Paired Duplicate Reads0000
Paired Optical Duplicate Reads0000
% Duplicate Reads39.880614.8714000000000012.56792.7032

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1ctl2
Total Reads8420985192350432913899532984314
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads8420985192350432913899532984314
Mapped Reads (QC-failed)0000
% Mapped Reads100.0100.0100.0100.0
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Filtered and duplicates removed


Sequence quality metrics (filtered/deduped BAM)

rep1
rep1
rep2
rep2

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.


Library complexity quality metrics


Library complexity (filtered non-mito BAM)

rep1rep2ctl1ctl2
Total Fragments14003748225926682990159133897537
Distinct Fragments8480552194581092922063133088144
Positions with Two Read23180532375148654199772743
NRF = Distinct/Total0.6055920.8612580.9772270.976122
PBC1 = OneRead/Distinct0.5718010.8599280.9771930.976145
PBC2 = OneRead/TwoRead2.0919247.04485543.64755141.797624

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline


NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally


Replication quality metrics


IDR (Irreproducible Discovery Rate) plots

rep1_vs_rep2
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
pooled-pr1_vs_pooled-pr2

Reproducibility QC and peak detection statistics

overlapidr
Nt9060231104
N13773119665
N211200335668
Np10860336023
N optimal10860336023
N conservative9060231104
Optimal Setpooled-pr1_vs_pooled-pr2pooled-pr1_vs_pooled-pr2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.19868214829694721.1581468621399178
Self Consistency Ratio2.9684609472317191.8137808288838038
Reproducibility Testborderlinepass

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks299967299982

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size184.0260.0224.0224.0
25 percentile736.01040.0459.0896.0
50 percentile (median)736.01040.0545.0896.0
75 percentile736.01040.0896.0896.0
Max size806.01493.01422.01422.0
Mean723.60923368237171000.1678234027376624.0377814174277801.2717972800015

rep1
rep1
rep2
rep2
idr_opt
idr_opt
overlap_opt
overlap_opt

Enrichment / Signal-to-noise ratio


Strand cross-correlation measures (trimmed/filtered SE BAM)

rep1rep2
Number of Subsampled Reads1400374815000000
Estimated Fragment Length525745
Cross-correlation at Estimated Fragment Length0.08293621483673590.137391245790004
Phantom Peak105105
Cross-correlation at Phantom Peak0.12832410.2422452
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.078811780.1334934
NSC (Normalized Strand Cross-correlation coeff.)1.0523331.029199
RSC (Relative Strand Cross-correlation coeff.)0.08330120.03584169


Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.


rep1
rep1
rep2
rep2

Jensen-Shannon distance (filtered/deduped BAM)

rep1rep2
AUC0.181309312964048620.22515871484068353
Synthetic AUC0.487667686918024870.4918224890168963
X-intercept0.36765388153421590.1639443266807983
Synthetic X-intercept1.7461346710229872e-551.4680587439249144e-127
Elbow Point0.65072391313042430.6452545694516658
Synthetic Elbow Point0.48951908903162120.498214439707471
JS Distance0.176813054116856050.22269305632898995
Synthetic JS Distance0.31128967924006920.35365931770311676
% Genome Enriched32.2749270087589527.074951005879296
Diff. Enrichment40.6653894602087230.77609702939294
CHANCE Divergence0.35723689854391350.2635657075904493

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.26420424689035780.25482688029343110.209509432743386570.27426940120334530.20915014207365790.274588742774775350.24008190908687250.251549336618451750.25143070085340535

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.12990972528665360.083187299347997890.14977382686381310.14513465201872083

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.082592879931998920.057629006582959120.085847741541310820.09048804839219862

For spp raw peaks:


For overlap/IDR peaks: